We aimed to clarify the changes in respiratory mechanics and factors associated with them in artificial pneumothorax two-lung ventilation in video-assisted thoracoscopic esophagectomy in the prone position (PP-VATS-E) for esophageal cancer. Data of patients with esophageal cancer, who underwent PP-VATs-E were retrospectively analyzed. Our primary outcome was the change in the respiratory mechanics after intubation (T1), in the prone position (T2), after initiation of the artificial pneumothorax two-lung ventilation (T3), at 1 and 2 h (T4 and T5), in the supine position (T6), and after laparoscopy (T7). The secondary outcome was identifying factors affecting the change in dynamic lung compliance (Cdyn). Sixty-seven patients were included. Cdyn values were significantly lower at T3, T4, and T5 than at T1 (p < 0.001). End-expiratory flow was significantly higher at T4 and T5 than at T1 (p < 0.05). Body mass index and preoperative FEV1.0% were found to significantly influence Cdyn reduction during artificial pneumothorax and two-lung ventilation (OR [95% CI]: 1.29 [1.03-2.24] and 0.20 (0.05-0.44); p = 0.010 and p = 0.034, respectively]. Changes in driving pressure were nonsignificant, and hypoxemia requiring treatment was not noted. This study suggests that in PP-VATs-E, artificial pneumothorax two-lung ventilation is safer for the management of anesthesia than conventional one-lung ventilation (UMIN Registry: 000042174).